maplepath := '${EXECUTABLE_MAPLE}': datadirname := '${DATA_DIRECTORY}': assigned := proc( a ) option builtin; 1 end: traperror := proc( expr ) option builtin; 2 end: eval := proc( expr ) option builtin; 3 end: If := proc( cond, exprtrue, exprfalse ) option builtin; 4 end: time := proc( expr ) option builtin; 5 end: noeval := proc( expr ) option builtin; 6 end: evalb := proc( BooleanExpr ) option builtin; 7 end: return := proc( returnvalues ) option builtin; 8 end: ReadLibrary := proc( filename, funcname ) option builtin; 9 end: zip := proc( expr ) option builtin; 10 end: sum := proc( a ) option builtin; 11 end: UTCTime := proc ( expr ) option builtin; 12 end: seq := proc( e ) option builtin; 13 end: remember := proc( f ) option builtin; 14 end: assert := proc( bool ) option builtin; 15 end: product := proc( a ) option builtin; 16 end: printf := proc( pattern:string ) option builtin; 50 end: prints := proc( ) for z in [args] do printf('%s\n',z) od end: error := proc( errormsgs ) option builtin; 51 end: iterate := proc( itervalue ) option builtin; 52 end: lprint := proc( toprint ) option builtin; 53 end: dprint := proc( toprint ) for i to nargs do if i >= 2 then printf( ',' ) fi; printf( '%A', args[i] ) od; lprint() end: FindLongestRep := proc( db:database, len:{posint,0}, endbonus:integer ) option builtin; 300 end: Match := proc( MatchParams ) option builtin; 55 end: max := proc( numbers ) option builtin, numeric; 56 end: min := proc( numbers ) option builtin, numeric; 57 end: CreateArray := proc( ranges, inivalue ) option builtin; 58 end: DrawPlot := proc() option builtin; 59 end: sort := proc( a:array, orderproc ) option builtin; 61 end: CreateString := proc( len:{posint,0}, inivalue:string ) option builtin; 301 end: op := proc( ) option builtin; 63 end: names := proc( typ:{type,'assigned'} ) option builtin; 302 end: ReadRawLine := proc( promptstring:string ) option builtin; 316 end: ReadLine := proc( promptstring:string ) option builtin; 303 end: CodonToInt := proc( UUU:string ) option builtin; 66 end: GetAllMatches := proc (m: Match, DM:DayMatrix, goal:numeric) option builtin; 169 end: sprintf := proc( pattern ) option builtin; 69 end: NucPepDynProg := proc( nuc: string, pep: string, DM: DayMatrix, len1: integer, len2: integer, IntronScoring: list ) option builtin; 305 end: append := proc(l:{list,structure,set}) option builtin; 71 end: TimedCallSystem := proc( command:string, timeout:posint ) option builtin; 307 end: LockFile := proc( filename:string, message:string ) option builtin; 308 end: MinSquareTree := proc( Dist: matrix(numeric), Var: matrix(numeric), Labels: list, Initial: {Tree,'Random','NJRandom','Trials'=posint}, Keep:'KeepTopology' ) option builtin; 266 end: LeastSquaresTree := ": Synteny_Invert := proc( p:list, i1:posint, i2:posint, mode:'InPlace' ) option builtin; 267 end: Synteny_FindOrders := proc( p:list ) option builtin; 268 end: Viterbi := proc( seq:list(posint), STS:{list(list(list(numeric))),SparsePFA}, S:list(numeric) ) option builtin; 270 end: ViterbiFast := proc( seq:list(posint), STS:{list(list(list(numeric))),SparsePFA}, S:list(numeric) ) option builtin; 271 end: ViterbiFast1 := proc( seq:list(posint), STS:{list(list(list(numeric))),SparsePFA}, S:list(numeric) ) option builtin; 272 end: SparsePFA_FixedPoint := proc( seq:list(list(posint)), spfa:SparsePFA ) option builtin; 273 end: CallExternal := proc(prog:string) option builtin; 74 end: ReadOffsetLine := proc( file:string, ofs:{0,posint} ) option builtin; 196 end: GetOffset := proc( t:string, df: database ) option builtin; 309 end: NucPepBackDynProg := proc( nuc: string, pep: string, DM: DayMatrix, len1: integer, len2: integer, IntronScoring: list ) option builtin; 306 end: NBody := proc (dist:matrix(numeric), var:matrix(numeric), k1:posint, k2:posint, rho1:numeric, rho2:numeric, inipos: matrix(numeric)) option builtin; 310 end: GetEntryNumber := proc( offset:{integer,string}, df: database ) option builtin; 311 end: type := proc( expr, typeval ) option builtin; 83 end: DynProgStrings := proc( m:{Match,Alignment}, dm:DayMatrix, noself:'NoSelf' ) option builtin; 85 end: SmallAllAll := noeval(ReadLibrary(SmallAllAll)): AlignOneAll := proc( seq:{string,posint}, db:database, day:DayMatrix, cutoff:numeric, entries: posint..posint ) option builtin; 314 end: Alignment := noeval(ReadLibrary(Align,Alignment)): Align := noeval(ReadLibrary(Align)): EstimateLogEvalue := noeval(ReadLibrary(Align,EstimateLogEvalue)): AToInt := proc( A:string ) option builtin; 100 end: IntToA := proc( P:posint ) option builtin; 101 end: AAAToInt := proc( AAA:string ) option builtin; 102 end: IntToAAA := proc( P:posint ) option builtin; 103 end: AminoToInt := proc( Amino:string ) option builtin; 104 end: IntToAmino := proc( P:posint ) option builtin; 105 end: type_type := proc(t) option internal; if t='type' then true else a := traperror(type(t,t)); a <> lasterror fi end: nonnegative_type := {0,positive}: DNA_type := {'A','C','G','T'}: RNA_type := {'A','C','G','U'}: # option zippable can be used for functions which do not have an interpretation # over matrices (other than zipping through). E.g. exp(), ln() abs := proc( x:numeric ) option builtin, numeric, zippable, polymorphic; 107 end: mod := proc( a:numeric, b:numeric ) option builtin, numeric, polymorphic; 108 end: iquo := proc(a:integer,b:integer) option polymorphic; trunc(a/b) end: sqrt := proc( x:numeric ) option builtin, numeric, zippable; 109 end: exp := proc( x:{numeric,matrix(numeric)} ) option builtin,polymorphic; 110 end: ln := proc( x:{numeric,matrix(numeric)} ) option builtin,polymorphic; 111 end: log := proc( x:{numeric,matrix(numeric)} ) option builtin,polymorphic; 111 end: ln1x := noeval(ReadLibrary(ln1x)): expx1 := noeval(ReadLibrary(ln1x,expx1)): length := proc( x ) option builtin; 112 end: TextHead := proc(x:string) option builtin; 113 end: round := proc( x:numeric ) option builtin, numeric, zippable; 114 end: sin := proc( x:numeric ) option builtin,numeric,polymorphic,zippable; 115 end: cos := proc( x:numeric ) option builtin,numeric,polymorphic,zippable; 116 end: tan := proc( x:numeric ) option builtin,numeric,polymorphic,zippable; 117 end: arcsin := proc(x:numeric) option builtin,numeric,polymorphic,zippable; 118 end: arccos := x -> Pi/2-arcsin(x): Rand := noeval(ReadLibrary(Rand)): Normal_Rand := proc( nr:structure ) options builtin, numeric; 88 end: Graph_Rand := noeval(ReadLibrary(Graph,Graph_Rand)): SetRand := proc( seed:integer ) option builtin; 120 end: RandL := proc( x:{list,set,string}) x[ceil(Rand()*length(x))] end: RandomSelection := noeval(ReadLibrary(RandomSelection)): OpenAppending := proc( filename:string ) option builtin; 121 end: OpenWriting := proc( filename:string ) option builtin; 122 end: GaussElim := proc( A:array(array(numeric)), b:array(numeric) ) option builtin; 123 end: SearchArray := proc( x, a:array ) option builtin; 124 end: sequal := proc( a, b ) option builtin; 125 end: CallSystem := proc( command:string ) option builtin; 126 end: ReadRawFile := proc( filename:string ) option builtin; 127 end: Set := proc( Option:{string,string=anything} ) option builtin; 128 end: parse := proc( x : string ) option builtin; 129 end: arctan := proc( y:numeric, x:numeric ) option builtin,numeric,polymorphic; 84 end: log10 := proc( x:{numeric,matrix(numeric)} ) t := ln(x); 0.0625*t + 0.0032055180967481723489*t; 0.5*t-" end: lg := proc( x:{numeric,matrix(numeric)} ) t := ln(x); 0.5*t - 0.05730495911103659264*t; t+" end: gc := proc() option builtin; 130 end: member := proc( x, s:{set,list,structure,identical(intersect())} ) option builtin; 131 end: version := proc() option builtin; 148 end: copy := proc( x:anything, depth:posint ) option builtin; 317 end: ceil := proc( x:numeric ) option builtin, numeric, zippable; 132 end: erf := proc( x:numeric ) option builtin, numeric, zippable; 133 end: erfc := proc( x:numeric ) option builtin, numeric, zippable; 134 end: floor := proc( x:numeric ) option builtin, numeric, zippable; 135 end: trunc := proc( x:numeric ) option builtin, numeric, zippable; 136 end: sscanf := proc( t:string, pat:string ) option builtin; 137 end: matrix_inverse := proc( A:matrix(numeric) ) option builtin; 138 end: transpose := proc( A:matrix ) option builtin; 139 end: Cholesky := proc( A:matrix(numeric) ) option builtin; 140 end: erfcinv := proc(y:numeric) option builtin, numeric,zippable; 141 end: scalb := proc( x:numeric, n:integer ) option builtin,numeric; 142 end: ilogb := proc( x:numeric ) option builtin,numeric, zippable; 143 end: ReadDb2 := proc( FileName:string ) option builtin, internal; 151 end: ReadDb := proc( FileName:string ) global DB; DB := remember( ReadDb2(FileName) ) end: CreateOrigDayMatrix := proc( Mutations:matrix(numeric), AaCounts:array(numeric), PamNumber:{numeric,1..posint} ) option builtin; 152 end: CaseSearchString := proc( pat:string, txt:string ) option builtin; 156 end: GetMostFrequentGrams := proc( n:posint, k:posint ) option builtin; 160 end: SearchDayMatrix := proc( PamNumber:numeric, DMS:array(DayMatrix) ) option builtin; 164 end: SearchDayIndex := noeval(ReadLibrary(SearchDayIndex)): CreateDayMatrix := proc( LogMutMatrix:matrix(numeric), PamNumber:{numeric,1..posint} ) option builtin; 165 end: SearchString := proc( pattern: string, text:string ) option builtin; 166 end: SearchMultipleString := noeval(ReadLibrary(SearchMultipleString)): SearchDelim := noeval(ReadLibrary(SearchDelim)): EnterProfile := proc( blockname:string ) option builtin; 167 end: ExitProfile := proc( blockname:string ) option builtin; 168 end: BToInt := proc( B:string ) option builtin; 170 end: NToInt := eval(BToInt): IntToB := proc( P:posint ) option builtin; 171 end: IntToN := eval(IntToB): BBBToInt := proc( BBB:string ) option builtin; 172 end: NucToInt := eval(BBBToInt): IntToBBB := proc( P:posint ) option builtin; 173 end: IntToNuc := eval(IntToBBB): BaseToInt := proc( Base:string ) option builtin; 174 end: NucleicToInt := eval(BaseToInt): IntToBase := proc( P:posint ) option builtin; 175 end: IntToNucleic := eval(IntToBase): SearchSeqDb := proc( t:{string,string..string} ) option builtin; 176 end: ProbDynProg := proc (A:array(array(numeric)), B:array(array(numeric)), f:array(numeric), w:posint, FixedDel:numeric, IncDel:numeric) option builtin; 179 end: date := proc( ) option builtin; 180 end: hostname := proc( ) option builtin; 181 end: ApproxSearchString := proc( pat:string, text:string, k:posint ) option builtin; 183 end: HammingSearchString := proc( pat:string, text:string, k:posint ) option builtin; 197 end: GetAllNucPepMatches := proc( npm: NucPepMatch, D:DayMatrix, goal: numeric ) option builtin; 184 end: AlignNucPepMatch := proc( npm: NucPepMatch, dm:DayMatrix ) option builtin; 185 end: FindNucPepPam := proc( npm: NucPepMatch, DMS:array(DayMatrix) ) option builtin; 186 end: SearchOrderedArray := proc( x, a:{array,string,structure} ) option builtin; 187 end: getpid := proc() option builtin; 188 end: sleep := proc( n:posint ) option builtin; 189 end: getenv := proc(varname: string) option builtin; 198 end: setenv := proc( name:string, value:string ) option builtin; 234 end: SearchTag := proc( tag:string, text:string ) option builtin; 190 end: SearchMassDb := proc( p:structure, n:integer ) option builtin; 191 end: DynProgMass := proc( p:{array, structure}, seq: string, stddev: numeric, deb: numeric ) option builtin; 192 end: DynProgMassDb := proc( p:array, m: integer, term: string, df: database, stddev: numeric, deb: numeric ) option builtin; 193 end: ReadProgram := proc( fname:string ) option builtin; 194 end: OpenReading := proc( fname:string ) option builtin; 195 end: union := proc(a:set,b:set) option builtin,polymorphic; 86 end: minus := proc(a:{set,identical(intersect())},b:{set,identical(intersect())}) option builtin,polymorphic; 201 end: intersect := proc(a:set, b:set) option builtin,polymorphic; 87 end: subset := proc(a:{set,identical(intersect())},b:{set,identical(intersect())}) option builtin; 203 end: OpenPipe := proc (cmd: string) option builtin; 106 end: hash := proc(s) option builtin; 149 end: hashstring := proc(s:string) option builtin; 150 end: has := proc(s,t) option builtin; 153 end: sha2 := proc(s) option builtin; 154 end: CurrentOff := proc () option builtin; 207 end: ConnectTcp := proc (path: string, slave: boolean) option builtin; 208 end: SendTcp := proc (data: string) option builtin; 209 end: ReceiveTcp := proc (timeout: {0, posint}) option builtin; 210 end: DisconnectTcp := proc () option builtin; 211 end: GetGramSiteScore := proc (n: string, S: GramSite) option builtin; 213 end: GetGramRegionScore := proc (n: string, S: GramRegion) option builtin; 214 end: EstimatePam := proc (s1: string, s2: string, DMS: array(DayMatrix)) option builtin; 215 end: DynProgNucPepString := proc( npm: NucPepMatch ) option builtin; 216 end: ParallelAllNucPepMatches := proc (npm: list(NucPepMatch), dm: {DayMatrix, list(DayMatrix)}, goal: numeric) option builtin; 224 end: antiparallel := proc (nuc: string) option builtin; 225 end: NucPepRegions := proc (npm: NucPepMatch) option builtin; 226 end: lowercase := proc(s: string) option builtin; 228 end: uppercase := proc(s: string) option builtin; 229 end: assemble := proc(s) option builtin; 230 end: disassemble := proc(s) option builtin; 231 end: display := noeval(ReadLibrary(display)): symbol := proc(s:{symbol,string}) option builtin; 232 end: warning := proc(s:string) option builtin; 233 end: ComputeTSP := noeval( ReadLibrary(ComputeTSP)): ComputeCubicTSP := proc( Dist:matrix, trials:posint, p1:list(posint) ) option builtin; 253 end: ComputeQuarticTSP := proc( Dist:matrix, trials:posint, p1:list(posint) ) option builtin; 254 end: Eigenvalues := proc( A:matrix, eigenvects:name ) option builtin; 252 end: VertexCover := proc( A:Graph ) option builtin; 255 end: VertexCover2 := proc( A:Graph, k : integer ) option builtin; 256 end: CliqueK := proc( A:Graph ) option builtin,internal; 257 end: Clique := noeval( ReadLibrary(Clique)): MaxEdgeWeightClique := proc( A:Graph ) option builtin; 265 end: MaxCut := noeval( ReadLibrary(MaxCut, MaxCut)): MinCut := noeval( ReadLibrary(MinCut)): MinimumCut := proc(g:Graph,trials:posint) option builtin; 274 end: factorial := proc(n:numeric) option builtin,numeric, zippable; 144 end: IntToAscii := proc (i:posint) option builtin; 155 end: AsciiToInt := proc (s:string) option builtin; 157 end: size := proc(s) option builtin; 147 end: Gamma := noeval( ReadLibrary(IncompleteGamma,Gamma)): LnGamma := noeval( ReadLibrary(IncompleteGamma,LnGamma)): Lngamma := noeval( ReadLibrary(IncompleteGamma,Lngamma)): debug := proc( arg:string ) option builtin; 315 end: assign := proc( a,v ) a := v; NULL end: CodonToA := proc () p := If (nargs = 3, CodonToInt(args[1], args[2], args[3]), CodonToInt(args[1])); If (p = 22, '$', IntToA(p)) end: enum := proc(n:{integer,integer..integer}) m := If (type (n, integer), 1..n, n); res := CreateArray (1..m[2]-m[1]+1); for i from m[1] to m[2] do res[i - m[1] + 1] := i od; res end: ReceiveDataTcp := noeval(ReadLibrary(IPC,ReceiveDataTcp)): ReadTcp := noeval(ReadLibrary(IPC,ReadTcp)): ReadData := noeval(ReadLibrary(ReadData,ReadData)): Readability := noeval(ReadLibrary(Readability)): SendDataTcp := noeval(ReadLibrary(IPC,SendDataTcp)): GetAaCount := noeval(ReadLibrary(AaCount,GetAaCount)): GetAaFrequency := noeval(ReadLibrary(AaFrequency)): CalculateScore := noeval(ReadLibrary(CalculateScore)): print := noeval(ReadLibrary(print)): Document := noeval(ReadLibrary(Document)): Table := noeval(ReadLibrary(Document,Table)): Code := noeval(ReadLibrary(Document,Code)): List := noeval(ReadLibrary(Document,List)): printtext := noeval(ReadLibrary(DBTools,printtext)): Paragraph := noeval(ReadLibrary(Document,Paragraph)): TextBlock := noeval(ReadLibrary(Document, TextBlock)): DocEl := noeval(ReadLibrary(Document, DocEl)): Indent := noeval(ReadLibrary(Document,Indent)): ConvertToEntityName := noeval(ReadLibrary(Document,ConvertToEntityName)): convolve := noeval(ReadLibrary(convolve)): GimpFigure := noeval(ReadLibrary(Document,GimpFigure)): PostscriptFigure := noeval(ReadLibrary(Document,PostscriptFigure)): PrintMatrix := noeval(ReadLibrary(print,PrintMatrix)): Primes := noeval(ReadLibrary(Iterators)): Indets := noeval(ReadLibrary(Iterators)): Infix := noeval(ReadLibrary(Iterators)): Prefix := noeval(ReadLibrary(Iterators)): Postfix := noeval(ReadLibrary(Iterators)): Leaves := noeval(ReadLibrary(Iterators)): Lines := noeval(ReadLibrary(Iterators)): Match_print := noeval(ReadLibrary(print,Match_print)): CreateDayMatrices := noeval(ReadLibrary(CreateDayMatrices)): DayMatrix := noeval(ReadLibrary(CreateDayMatrices,DayMatrix)): Identity := noeval(ReadLibrary(Identity)): SearchDb := noeval(ReadLibrary(SearchDF,SearchDb)): SearchID := noeval(ReadLibrary(SearchDF,SearchID)): SearchAC := noeval(ReadLibrary(SearchDF,SearchAC)): GetEntryInfo := noeval(ReadLibrary(EntryInfo)): PrintInfo := noeval(ReadLibrary(EntryInfo,PrintInfo)): PatEntry := noeval(ReadLibrary(Entries,PatEntry)): Entry := noeval(ReadLibrary(Entries,Entry)): Entries := noeval(ReadLibrary(Entries)): Sequence := noeval(ReadLibrary(Entries,Sequence)): Sequences := noeval(ReadLibrary(Entries,Sequences)): SequenceComplexity := noeval(ReadLibrary(SequenceComplexity)): string := noeval(ReadLibrary(Entries,string)): table := noeval(ReadLibrary(table)): SplitLines := noeval(ReadLibrary(SplitLines)): ID := noeval(ReadLibrary(Entries,ID)): atoi := noeval(ReadLibrary(atoi)): CreateRandPermutation := noeval(ReadLibrary(RandomPermut)): Permutation := noeval(ReadLibrary(Permutation)): Shuffle := noeval(ReadLibrary(RandomPermut,Shuffle)): SetRandSeed := noeval(ReadLibrary(RandomPermut,SetRandSeed)): Mutate := noeval(ReadLibrary(RandomPermut,Mutate)): CreateRandSeq := noeval(ReadLibrary(RandomPermut,CreateRandSeq)): Stat := noeval(ReadLibrary(Stat)): Counter := noeval(ReadLibrary(Counter)): StatTest := noeval(ReadLibrary(StatTest)): TestGradHessian := noeval(ReadLibrary(TestGradHessian)): Zscore := noeval(ReadLibrary(Zscore)): ZscorePercent := noeval(ReadLibrary(Zscore,ZscorePercent)): avg := noeval(ReadLibrary(Stat,avg)): var := noeval(ReadLibrary(Stat,var)): std := noeval(ReadLibrary(Stat,std)): CollectStat := noeval(ReadLibrary(Stat,CollectStat)): Polar := noeval(ReadLibrary(Polar)): UpdateStat := noeval(ReadLibrary(Stat,UpdateStat)): OutsideBounds := noeval(ReadLibrary(OutsideBounds)): LinearRegression := noeval(ReadLibrary(Stat,LinearRegression)): Covariance := noeval(ReadLibrary(Covariance)): Cumulative := noeval(ReadLibrary(Cumulative)): CumulativeStd := noeval(ReadLibrary(Cumulative,CumulativeStd)): Std_Score := noeval(ReadLibrary(Cumulative,Std_Score)): ExpFit := noeval(ReadLibrary(Stat,ExpFit)): ExpFit2 := noeval(ReadLibrary(Stat,ExpFit2)): MaxLikelihoodSize := noeval(ReadLibrary(Stat,MaxLikelihoodSize)): ProbBallsBoxes := noeval(ReadLibrary(ProbBallsBoxes)): lnProbBallsBoxes := noeval(ReadLibrary(ProbBallsBoxes,lnProbBallsBoxes)): ProbCloseMatches := noeval(ReadLibrary(ProbBallsBoxes,ProbCloseMatches)): PerIdentToPam := noeval(ReadLibrary(PItoPam)): PamToPerIdent := noeval(ReadLibrary(PItoPam,PamToPerIdent)): DrawGraph := noeval(ReadLibrary(Graph,DrawGraph)): DrawHistogram := noeval(ReadLibrary(Histogram)): DrawDistribution := noeval(ReadLibrary(Histogram,DrawDistribution)): DrawDotplot := noeval(ReadLibrary(Histogram,DrawDotplot)): DrawPointDistribution := noeval(ReadLibrary(Histogram,DrawPointDistribution)): SmoothData := noeval(ReadLibrary(Histogram,SmoothData)): DrawStackedBar := noeval(ReadLibrary(Histogram,DrawStackedBar)): ViewPlot := noeval(ReadLibrary(Histogram,ViewPlot)): Plot2Gif := noeval(ReadLibrary(Plot2Gif)): View := noeval(ReadLibrary(View)): SystemCommand := noeval(ReadLibrary(SystemCommand)): StartOverlayPlot := noeval(ReadLibrary(Histogram,StartOverlayPlot)): StopOverlayPlot := noeval(ReadLibrary(Histogram,StopOverlayPlot)): GetColorMap := noeval(ReadLibrary(Histogram,GetColorMap)): DrawTree := noeval(ReadLibrary(DrawPackage,DrawTree)): string_RGB := noeval(ReadLibrary(Color,string_RGB)): RGB_string := noeval(ReadLibrary(Color,RGB_string)): ColorPalette := noeval(ReadLibrary(Color,ColorPalette)): BrightenColor := noeval(ReadLibrary(Color,BrightenColor)): CrossReference := noeval(ReadLibrary(CrossReference)): ShortNames := noeval(ReadLibrary(CrossReference,ShortNames)): CollapseNodes := noeval(ReadLibrary(SummarizeTree)): PrintTreeSeq := noeval(ReadLibrary(SummarizeTree,PrintTreeSeq)): SearchFrag := noeval(ReadLibrary(SearchFrag)): GetMolWeight := noeval(ReadLibrary(MolWeight,GetMolWeight)): NucPepMatch := noeval(ReadLibrary(NPMatch)): NucPepMatch_print := noeval(ReadLibrary(NPMatch, NucPepMatch_print)): LocalNucPepAlign := noeval(ReadLibrary(NPMatch,LocalNucPepAlign)): GlobalNucPepAlign := noeval(ReadLibrary(NPMatch,GlobalNucPepAlign)): LocalNucPepAlignBestPam := noeval(ReadLibrary(NPMatch,LocalNucPepAlignBestPam)): GetPeptides := noeval(ReadLibrary(NPMatch,GetPeptides)): GetIntrons := noeval(ReadLibrary(NPMatch,GetIntrons)): AlignNucPepAll := noeval(ReadLibrary(NPMatch,AlignNucPepAll)): VisualizeGene := noeval(ReadLibrary(NPMatch,VisualizeGene)): NucID := noeval(ReadLibrary(NPMatch,NucID)): MaximizeFunc := noeval(ReadLibrary(Maximize)): MaximizeRD := noeval(ReadLibrary(Maximize)): BestSearchString := noeval(ReadLibrary(BestStringMatch)): PrintStringMatch := noeval(ReadLibrary(BestStringMatch,PrintStringMatch)): Matrices := noeval(ReadLibrary(Matrices)): FindEntropy := noeval(ReadLibrary(Matrices,FindEntropy)): DayMatrixScale := noeval(ReadLibrary(Matrices,DayMatrixScale)): ParExecuteIPC := noeval(ReadLibrary(ParExec2)): GetMachineUsage := noeval(ReadLibrary(ParExec2,GetMachineUsage)): ParExecuteTest := noeval(ReadLibrary(ParExec2,ParExecuteTest)): ParExecSlave := noeval(ReadLibrary(ParExecSlave)): MinimizeFunc := noeval(ReadLibrary(Minimize)): DisconMinimize := noeval(ReadLibrary(Minimize,DisconMinimize)): BFGSMinimize := noeval(ReadLibrary(BFGSMinimize,BFGSMinimize)): Minimize2DFunc := noeval(ReadLibrary(Minimize,Minimize2DFunc)): MinimizePWC := noeval(ReadLibrary(Minimize,MinimizePWC)): MinimizeSD := noeval(ReadLibrary(Minimize,MinimizeSD)): MinimizeBrent := noeval(ReadLibrary(Minimize,MinimizeBrent)): DbToDarwin := noeval(ReadLibrary(ConvertToDF)): SpToDarwin := noeval(ReadLibrary(ConvertSP)): sign := noeval(ReadLibrary(sign)): Zeta := noeval(ReadLibrary(Zeta)): Graph := noeval(ReadLibrary(Graph)): TetrahedronGraph := noeval(ReadLibrary(Graph,TetrahedronGraph)): HexahedronGraph := noeval(ReadLibrary(Graph,HexahedronGraph)): CubeGraph := noeval(ReadLibrary(Graph,CubeGraph)): OctahedronGraph := noeval(ReadLibrary(Graph,OctahedronGraph)): IcosahedronGraph := noeval(ReadLibrary(Graph,IcosahedronGraph)): DodecahedronGraph := noeval(ReadLibrary(Graph,DodecahedronGraph)): PetersenGraph := noeval(ReadLibrary(Graph,PetersenGraph)): BipartiteGraph := noeval(ReadLibrary(Graph,BipartiteGraph)): BipartiteMatching := noeval(ReadLibrary(BipartiteMatching)): Complete := noeval(ReadLibrary(Graph,Complete)): RegularGraph := noeval(ReadLibrary(Graph,RegularGraph)): Edge := noeval(ReadLibrary(Graph,Edge)): EdgeComplement := noeval(ReadLibrary(Graph,EdgeComplement)): ShortestPath := noeval(ReadLibrary(Graph,ShortestPath)): InduceGraph := noeval(ReadLibrary(Graph,InduceGraph)): FindConnectedComponents := noeval(ReadLibrary(Graph,FindConnectedComponents)): ParseDimacsGraph := noeval(ReadLibrary(Graph, ParseDimacsGraph)): Tree := noeval(ReadLibrary(Tree)): TreeResult := noeval(ReadLibrary(TreeResult)): RellTree := noeval(ReadLibrary(TreeResult)): AllAllResult := noeval(ReadLibrary(TreeResult,AllAllResult)): AlSumm := noeval(ReadLibrary(TreeResult,AlSumm)): GetTreeLabels := noeval(ReadLibrary(Tree,GetTreeLabels)): DigestSeq := noeval(ReadLibrary(MassProfile,DigestSeq)): DigestWeights := noeval(ReadLibrary(MassProfile,DigestWeights)): Gene := noeval(ReadLibrary(Gene)): GetComplement := noeval(ReadLibrary(Gene,GetComplement)): ComplementSequence := noeval(ReadLibrary(Gene,ComplementSequence)): Complement := noeval(ReadLibrary(Gene,Complement)): Reverse := noeval(ReadLibrary(Gene,Reverse)): help := noeval(ReadLibrary(help)): IntronModel := noeval(ReadLibrary(IntronScores,IntronModel)): LinearIntron := noeval(ReadLibrary(IntronScores,LinearIntron)): Intron := noeval(ReadLibrary(IntronScores,Intron)): Fold := noeval(ReadLibrary(Fold)): ReadBrk := noeval(ReadLibrary(Fold,ReadBrk)): ReadDssp := noeval(ReadLibrary(Fold,ReadDssp)): CreateCProgram := noeval(ReadLibrary(ExtCallFrame)): PredictGenes := noeval(ReadLibrary(PredictGenes)): PamWindows := noeval(ReadLibrary(StructurePrediction,PamWindows)): SurfIntActPred := noeval(ReadLibrary(StructurePrediction,SurfIntActPred)): ParsePred := noeval(ReadLibrary(StructurePrediction,ParsePred)): PrintPV := noeval(ReadLibrary(ProbModel,PrintPV)): MostProbAA := noeval(ReadLibrary(ProbModel,MostProbAA)): ProbTree := noeval(ReadLibrary(ProbModel,ProbTree)): ConvertTree := noeval(ReadLibrary(ProbModel,ConvertTree)): # Added 05.02.97, Chantal Korostensky WriteFasta := noeval(ReadLibrary(FileConv, WriteFasta)): ReadMap := noeval(ReadLibrary(FileConv, ReadMap)): ReadFasta := noeval(ReadLibrary(FileConv, ReadFasta)): ReadPir := noeval(ReadLibrary(FileConv, ReadPir)): ReadPima := noeval(ReadLibrary(FileConv, ReadPima)): ReadMsa := noeval(ReadLibrary(FileConv, ReadMsa)): IdenticalTrees := noeval(ReadLibrary(TreeUtil, IdenticalTrees)): GetMATreeNew := noeval(ReadLibrary(TreeUtil, GetMATreeNew)): UnlabelLeaves := noeval(ReadLibrary(TreeUtil, UnlabelLeaves)): AddSpecies := noeval(ReadLibrary(TreeUtil, AddSpecies)): FindRules := noeval(ReadLibrary(TreeUtil, FindRules)): FindSpeciesViolations := noeval(ReadLibrary(TreeUtil, FindSpeciesViolations)): GetPathDistance := noeval(ReadLibrary(TreeUtil, GetPathDistance)): TotalTreeWeight := noeval(ReadLibrary(TreeUtil, TotalTreeWeight)): FindCircularOrder := noeval(ReadLibrary(Tree, FindCircularOrder)): CircularTour := noeval(ReadLibrary(CircularTour)): Clusters := noeval(ReadLibrary(CircularTour,Clusters)): Species_Entry := noeval(ReadLibrary(Species,Species_Entry)): SP_Species := noeval(ReadLibrary(Species,SP_Species)): SPCommonName := noeval(ReadLibrary(Species,SPCommonName)): Orthologues := noeval(ReadLibrary(Orthologues)): PhylogeneticTree := noeval(ReadLibrary(PhylogeneticTree)): GapTree := noeval(ReadLibrary(GapTree)): OptimizeTree := noeval(ReadLibrary(PhylogeneticTree,OptimizeTree)): RBFS_Tree := noeval(ReadLibrary(RBFS_tree)): ComputeDimensionlessFit := noeval(ReadLibrary(RBFS_tree,ComputeDimensionlessFit)): RemoveUnchanged := noeval(ReadLibrary(PhylogeneticTree,RemoveUnchanged)): Synteny := noeval(ReadLibrary(Synteny)): SignedSynteny := noeval(ReadLibrary(SignedSynteny)): dSplits := noeval(ReadLibrary(dSplits)): KWIndex := noeval(ReadLibrary(VariationIndices,KWIndex)): ProbIndex := noeval(ReadLibrary(VariationIndices,ProbIndex)): ScaleIndex := noeval(ReadLibrary(VariationIndices,ScaleIndex)): PrintIndex := noeval(ReadLibrary(VariationIndices,PrintIndex)): PlotIndex := noeval(ReadLibrary(VariationIndices,PlotIndex)): ParseNewickTree := noeval(ReadLibrary(Newick2Darwin, ParseNewickTree)): BinaryNewick2Darwin := noeval(ReadLibrary(Newick2Darwin, BinaryNewick2Darwin)): # Added 10.02.97, Chantal Korostensky HTMLC := noeval(ReadLibrary(HTMLCTools, HTMLC)): HTML := noeval(ReadLibrary(HTMLCTools, HTML)): HyperLink := noeval(ReadLibrary(HTMLCTools, HyperLink)): PlusMin := noeval(ReadLibrary(HTMLCTools, PlusMin)): HTMLColor := noeval(ReadLibrary(HTMLTools, HTMLColor)): Center := noeval(ReadLibrary(HTMLCTools,Center)): WeightObservations := noeval(ReadLibrary(WeightObservations)): SVD := noeval(ReadLibrary(SVD)): SvdResult := noeval(ReadLibrary(SvdAnalysis,SvdResult)): SvdAnalysis := noeval(ReadLibrary(SvdAnalysis)): SvdBestBasis := noeval(ReadLibrary(SvdBestBasis)): LinearClassify := noeval(ReadLibrary(LinearClassify)): LinearClassification := noeval(ReadLibrary(LinearClassify,LinearClassification)): LinearProgramming := noeval(ReadLibrary(LinearProgramming)): CreateDB := noeval(ReadLibrary(DBTools, CreateDB)): Description := noeval(ReadLibrary(Description)): HelpEntry := noeval(ReadLibrary(Description,HelpEntry)): Descriptions := noeval(ReadLibrary(Descriptions)): mselect := noeval(ReadLibrary(AlgManipulation,mselect)): hastype := noeval(ReadLibrary(AlgManipulation,hastype)): indets := noeval(ReadLibrary(AlgManipulation,indets)): algebraic_type := noeval(ReadLibrary(AlgManipulation,algebraic_type)): subs := noeval(ReadLibrary(AlgManipulation,subs)): coeff := noeval(ReadLibrary(AlgManipulation,coeff)): lcoeff := noeval(ReadLibrary(AlgManipulation,lcoeff)): gcd := noeval(ReadLibrary(AlgManipulation,gcd)): PartialFraction := noeval(ReadLibrary(AlgManipulation,PartialFraction)): LongInteger := noeval(ReadLibrary(LongInteger)): Complex := noeval(ReadLibrary(Complex)): Inherit := noeval(ReadLibrary(Inherit)): ExtendClass := noeval(ReadLibrary(Inherit,ExtendClass)): Protect := noeval(ReadLibrary(Inherit,Protect)): GetMethods := noeval(ReadLibrary(Inherit,GetMethods)): CompleteClass := noeval(ReadLibrary(Inherit,CompleteClass)): Introspection := noeval(ReadLibrary(Inherit,Introspection)): list_power := noeval(ReadLibrary(list_power)): set_power := noeval(ReadLibrary(set_power)): GramSchmidt := noeval(ReadLibrary(GramSchmidt)): GivensElim := noeval(ReadLibrary(GivensElim)): gigahertz := noeval(ReadLibrary(gigahertz)): LSBestSum := noeval(ReadLibrary(LSBestSum)): LSBestDelete := noeval(ReadLibrary(LSBestSum,LSBestDelete)): LSBestSumDelete := noeval(ReadLibrary(LSBestSum,LSBestSumDelete)): ContinuedFraction := noeval(ReadLibrary(ContinuedFraction)): # *** ADDED FROM CH.K, 3.8.98 *** MSAMethod := noeval(ReadLibrary(MSAParameters, MSAMethod)): MSAStatistics := noeval(ReadLibrary(MSAParameters, MSAStatistics)): MSA_CT := noeval(ReadLibrary(MSA_CT)): Gap := noeval(ReadLibrary(GapH, Gap)): GapHeuristic := noeval(ReadLibrary(GapH, GapHeuristic)): DoGapHeuristic := noeval(ReadLibrary(GapH, DoGapHeuristic)): TreeConstruction := noeval(ReadLibrary(TreeParameters, TreeConstruction)): rawprint := noeval(ReadLibrary(TreeParameters, rawprint)): TreeStatistics := noeval(ReadLibrary(TreeParameters, TreeStatistics)): Partitions := noeval(ReadLibrary(Partitions, Partitions)): ResolveConflicts := noeval(ReadLibrary(Partitions, ResolveConflicts)): GetConflicts := noeval(ReadLibrary(Partitions, GetConflicts)): GetTree := noeval(ReadLibrary(Tree, GetTree)): ChangeLeafLabels := noeval(ReadLibrary(Tree, ChangeLeafLabels)): GetPartitions := noeval(ReadLibrary(Partitions, GetPartitions)): #CreateRandMultAlign := noeval(ReadLibrary(RandomMSA, CreateRandMultAlign)): CreateRandMultAlign := noeval(ReadLibrary(RandomMSA)): LLL := noeval(ReadLibrary(LLL)): GapMatch := noeval(ReadLibrary(DynProgGap, GapMatch)): DynProgGap := noeval(ReadLibrary(DynProgGap, DynProgGap)): Roman := noeval(ReadLibrary(Roman)): Alphabetical := noeval(ReadLibrary(Roman,Alphabetical)): Alphanumerical := noeval(ReadLibrary(Roman,Alphanumerical)): Ordinal := noeval(ReadLibrary(Roman,Ordinal)): # *** Parsimony_merge_e := proc( x, y ) option builtin, internal; 241 end: Parsimony_cost_e := proc( x, y ) option builtin, internal; 242 end: compress := proc( x ) option builtin; 243 end: decompress := proc( x ) option builtin; 244 end: DynProgRowSpecial := proc( rf:array(list,2), rf1:array(list,2), iSeq2:list, sco:list, C0:numeric, C1:numeric, minscore:numeric ) option builtin; 245 end: ServerSocket_internal := proc( socket_path:string ) option builtin, internal; 246 end: ServerSocket := proc( socket_path:string; (gcf=10^10):posint ) Set(quiet=true); Set(batch=true); Set(gc=gcf); ServerSocket_internal( args ); end: exit := proc(e:{0,posint}) option builtin; 247 end: FileStat := noeval(ReadLibrary(FileStat)): NormalizePath := noeval(ReadLibrary(FileStat, NormalizePath)): LinearClassify_X0 := proc( AX:list(numeric), wneg:numeric, wpos:numeric, sb:posint, b:list, ind0:name ) option builtin; 259 end: DynProgScore := proc( seq1:{string,structure}, seq2:{string,structure}, dm:DayMatrix, modif:{string,structure,set({string,structure})} ) option builtin; 260 end: DynProgBoth := proc( seq1:string, seq2:string, dm:DayMatrix, modif:{string,structure,set({string,structure})} ) option builtin; 269 end: TPIDistr := proc( m1:{0,posint}, m2:{0,posint}, m3:{0,posint}, m4:{0,posint} ) option builtin; 261 end: LinearClassification_DirOpt2 := proc( AX:list, Adx:list, wneg:numeric, wpos:numeric, sb:posint, b:list(integer) ) option builtin; 262 end: LinearClassification_DirOpt3 := proc( AX:list, Adx:list, wneg:numeric, wpos:numeric, sb:posint, b:list(integer) ) option builtin; 263 end: LinearClassification_DirOpt4 := proc( AX:list, Adx:list, wneg:numeric, wpos:numeric, sb:posint, b:list(integer) ) option builtin; 264 end: ComputeTPI := noeval(ReadLibrary(ComputeTPI)): TotalAlign := proc( m:Match, DM:DayMatrix, goal:numeric ) option builtin; 178 end: #from florida Marcel Turcotte ExpandFileName := noeval(ReadLibrary(MBA_Toolkit, ExpandFileName)): ReadFastaWithNames := noeval(ReadLibrary(MBA_Toolkit, ReadFastaWithNames)): WriteDarwinDb := noeval(ReadLibrary(MBA_Toolkit,WriteDarwinDb)): FastaToDarwinDb := noeval(ReadLibrary(MBA_Toolkit,FastaToDarwinDb)): # Stefan Zoller, Aug 2011 ReadPhylip := noeval(ReadLibrary(MBA_Toolkit, ReadPhylip)): #codon stuff gmc Aug 2, 2001 AToCodon := noeval(ReadLibrary(CodonTools, AToCodon)): IntToCodon := noeval(ReadLibrary(CodonTools, IntToCodon)): #CodonToInt := noeval(ReadLibrary(CodonTools, CodonToInt)): CIntToInt := noeval(ReadLibrary(CodonTools, CIntToInt)): CIntToA := noeval(ReadLibrary(CodonTools, CIntToA)): CodonToAAA := noeval(ReadLibrary(CodonTools, CodonToAAA)): CIntToAAA := noeval(ReadLibrary(CodonTools, CIntToAAA)): CodonToAmino := noeval(ReadLibrary(CodonTools, CodonToAmino)): CIntToAmino := noeval(ReadLibrary(CodonTools, CIntToAmino)): AltGenCode := noeval(ReadLibrary(CodonTools, AltGenCode)): CodonToCInt := noeval(ReadLibrary(CodonTools, CodonToCInt)): SetuptRNA := noeval(ReadLibrary(SetuptRNA)): NucToCode := noeval(ReadLibrary(CodonTools,NucToCode)): CodeToNuc := noeval(ReadLibrary(CodonTools,CodeToNuc)): CIntToCodon := noeval(ReadLibrary(CodonTools,CIntToCodon)): AToCInt := noeval(ReadLibrary(CodonTools,AToCInt)): IntToCInt := noeval(ReadLibrary(CodonTools,IntToCInt)): #dna stuff gmc Aug 5, 2002 CheckDNA := noeval(ReadLibrary(DNATools, CheckDNA)): CreateDNAAlignFromProtein := noeval(ReadLibrary(DNATools, CreateDNAAlignFromProtein)): CreateUngappedSequence := noeval(ReadLibrary(DNATools, CreateUngappedSequence)): CreateProteinAlignFromDNA := noeval(ReadLibrary(DNATools, CreateProteinAlignFromDNA)): ConsistentGenome := noeval(ReadLibrary(ConsistentGenome)): GenomeSummary := noeval(ReadLibrary(GenomeSummary)): #counting bases, SearchAllArray, PvR, Feb 20, 2003 BaseCount := noeval(ReadLibrary(CodonCountsLib,BaseCount)): SearchAllArray := noeval(ReadLibrary(SearchAllArray)): # # Number of accepted point mutations, from: # A Model of Evolutionary Change in Proteins by # M.O. Dayhoff, R.M. Schwartz and B.C. Orcutt. Mutations1978 := [ [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [ 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [109, 17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [154, 0,532, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [ 33, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [ 93,120, 50, 76, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [266, 0, 94,831, 0,422, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [579, 10,156,162, 10, 30,112, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [ 21,103,226, 43, 10,243, 23, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [ 66, 30, 36, 13, 17, 8, 35, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [ 95, 17, 37, 0, 0, 75, 15, 17, 40,253, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [ 57,477,322, 85, 0,147,104, 60, 23, 43, 39, 0, 0, 0, 0, 0, 0, 0, 0, 0], [ 29, 17, 0, 0, 0, 20, 7, 7, 0, 57,207, 90, 0, 0, 0, 0, 0, 0, 0, 0], [ 20, 7, 7, 0, 0, 0, 0, 17, 20, 90,167, 0, 17, 0, 0, 0, 0, 0, 0, 0], [345, 67, 27, 10, 10, 93, 40, 49, 50, 7, 43, 43, 4, 7, 0, 0, 0, 0, 0, 0], [772,137,432, 98,117, 47, 86,450, 26, 20, 32,168, 20, 40,269, 0, 0, 0, 0, 0], [590, 20,169, 57, 10, 37, 31, 50, 14,129, 52,200, 28, 10, 73,696, 0, 0, 0, 0], [ 0, 27, 3, 0, 0, 0, 0, 0, 3, 0, 13, 0, 0, 10, 0, 17, 0, 0, 0, 0], [ 20, 3, 36, 0, 30, 0, 10, 0, 40, 13, 23, 10, 0,260, 0, 22,23, 6, 0, 0], [365, 20, 13, 17, 33, 27, 37, 97, 30,661,303, 17, 77, 10, 50, 43,186,0,17,0]]: DBL_EPSILON := 2.2204460492503131*10^(-16): DBL_MAX := 1.7976931348623147*10^308: Pi := -0.32584135910528735661672e-06 + 3294199/1048576: # Matrix generated on Mon Nov 4 05:29:35 MET 1991 # from sample with PAM from 6.4 to 100.0 extrapolated to 116.5 # random vs random gives -0.62196 similarity NewLogPAM1 := [[ -94849167.5024, 4544331.5392, 3950895.7642, 5075559.2685, 10509486.6552, 7821215.6793, 9284867.4577, 10208268.6773, 4128730.4460, 2088402.6725, 3942030.3556, 5544102.9591, 7873192.1288, 2081786.9806, 8933017.3353, 25463979.0926, 12087687.9616, 938717.6754, 1816599.3219, 14779792.0604], [ 3088606.9019, -79929382.8416, 4269239.6312, 1655233.1266, 1736199.9907, 13919517.8286, 3630902.6919, 2602718.2624, 6947846.1049, 926558.7304, 1807263.7386, 25753650.3430, 1710966.8045, 350093.8734, 2237195.6388, 4166759.1691, 3978330.3745, 3253232.5391, 2289634.0815, 1544649.7457], [ 2290927.3283, 3642282.6431, -96451119.9812, 15734455.2696, 1516899.1156, 7178694.2982, 4353788.4775, 4771506.9422, 11545580.2546, 1102105.6247, 656762.2820, 8464648.9678, 1137719.5856, 878876.5516, 1538902.9216, 11023119.2471, 6900696.3646, 570925.9280, 2766153.3106, 743887.8388], [ 3470266.3186, 1665119.6347, 18553031.1074, -81923956.4087, 276028.4793, 6226313.0607, 24312537.5194, 4134242.6743, 5282013.4703, 188341.4823, 131158.4714, 4149263.8609, 236419.6850, 223657.2420, 2479252.1442, 6226729.7105, 4557332.3643, 77176.2019, 1205027.7108, 179487.3608], [ 2522064.2915, 613030.0599, 627791.7545, 96883.4602, -46823529.9064, 216095.4307, 43613.4399, 489113.7805, 995254.8196, 447266.9547, 570876.9633, 71989.8710, 1127983.9013, 1033868.3428, 73686.9290, 2295153.6442, 1121976.9695, 928124.3635, 1279520.8909, 1884650.4311], [ 3754699.1282, 9831786.5667, 5943340.3069, 4371725.9675, 432286.6396, -124298615.8968, 15604785.8586, 1690312.4338, 12104211.9812, 843586.2680, 2606859.1297, 12493678.3810, 5420375.2816, 755560.3559, 3509155.2648, 4707458.9403, 4148983.1610, 1264258.7211, 1249105.6978, 1313424.8190], [ 6901386.7806, 3970842.3038, 5581002.8430, 26430905.7693, 135084.7585, 24161149.5137, -95466922.2113, 2105215.6424, 5809977.3792, 952630.9241, 906956.1549, 12697999.5654, 2157145.3021, 276111.1317, 3465447.4123, 5784171.0817, 4183806.0648, 556528.0589, 958942.6584, 2712747.7789], [ 9555577.7381, 3584589.1700, 7702730.0356, 5660071.5590, 1907831.9028, 3295876.7633, 2651189.5986, -41190659.0280, 2465528.1371, 211987.5938, 491124.0624, 2569041.9933, 1091377.8601, 377442.8186, 2051441.8768, 8478517.4003, 1831897.2059, 1404167.8359, 688481.4858, 704639.7340], [ 1236548.8172, 3061627.1303, 5963411.2455, 2313744.1798, 1242093.7478, 7551450.4635, 2341038.2998, 788859.8300, -90660120.4886, 588718.8936, 732377.8326, 2803016.8479, 1554270.9098, 1775938.6189, 1066164.1001, 1921603.5205, 2153123.2181, 1046731.2440, 7786680.5888, 447060.1420], [ 1543249.4441, 1007400.6166, 1404524.6535, 203558.3731, 1377254.0280, 1298525.5848, 947078.3419, 167350.6781, 1452563.4971, -105165666.0254, 18851556.4458, 1878072.3685, 22933389.7197, 5722207.3179, 885057.0022, 1172267.0207, 4582762.4974, 1465194.3072, 2107443.0141, 36788470.9311], [ 4735652.4519, 3194396.0762, 1360668.4663, 230450.3133, 2857772.9813, 6523438.0370, 1465836.3636, 630298.4116, 2937651.7630, 30646803.3616, -70057672.5190, 2984548.3113, 41990207.1426, 19031758.3366, 3378475.8298, 2163507.1296, 3252921.6763, 4222106.5048, 4605829.1937, 16061545.5607], [ 4152442.7343, 28380401.2191, 10933660.2953, 4545320.5538, 224682.4288, 19492242.5698, 12795198.0861, 2055600.4789, 7009763.0300, 1903543.4708, 1860763.2506, -100965731.1416, 4352426.8576, 470289.9972, 3370756.0739, 5565187.5825, 7473159.9932, 435422.0564, 1721791.4731, 1965467.6037], [ 2286382.4161, 731049.8231, 569793.5322, 100415.9623, 1364979.9529, 3278887.3660, 842784.9318, 338585.4592, 1507058.1294, 9012481.4582, 10150470.6780, 1687551.9006, -122250535.0004, 4432083.6764, 149239.9440, 1329648.9217, 2331130.0096, 1018524.1197, 1055358.4070, 3460802.9081], [ 1080457.2558, 267339.5323, 786653.4267, 169775.6359, 2235948.9789, 816844.8685, 192794.4640, 209275.1254, 3077545.7446, 4018953.6882, 8222243.9644, 325885.2310, 7921022.2187, -66575606.6139, 385382.2694, 546638.3440, 1161001.0985, 9013061.4954, 23971713.5077, 2358959.7055], [ 5187462.7012, 1911472.9004, 1541176.1992, 2105710.2259, 178308.7342, 4244812.5339, 2707418.9482, 1272656.4091, 2067217.2896, 695514.4604, 1633118.7637, 2613435.4097, 298430.9531, 431198.4966, -49432932.9748, 5421906.4901, 4429139.5737, 241454.6074, 844692.9784, 1353701.1962], [ 19589024.4498, 4716201.0426, 14624307.2847, 7005959.9761, 7357387.8850, 7543487.9401, 5986417.6133, 6967894.9909, 4935777.6656, 1220369.0856, 1385431.3541, 5716023.1857, 3522293.1905, 810243.0773, 7182601.1733, -119150506.2689, 27955884.4072, 1515129.0644, 3323057.5421, 1912272.3447], [ 9500142.4571, 4600394.6942, 9353282.5694, 5238641.4917, 3674482.3830, 6792469.0774, 4423823.2151, 1538094.8555, 5650163.6266, 4874076.4730, 2128142.1131, 7841854.7268, 6308924.7995, 1758118.7508, 5994451.2590, 28561010.8460, -104950600.4902, 717314.3721, 1760999.6535, 10434752.8601], [ 156259.3029, 796770.7189, 163898.4750, 18789.5071, 643787.3073, 438375.1885, 124634.2181, 249703.7416, 581770.0213, 330053.4075, 585032.7973, 96771.8284, 583827.0101, 2890759.2177, 69213.3028, 327849.0859, 151926.5032, -38106197.0662, 3439097.9644, 154814.9186], [ 757720.7584, 1405152.5941, 1989805.1163, 735136.8110, 2223938.4753, 1085296.3624, 538123.5728, 306787.3482, 10844453.2596, 1189553.5260, 1599182.4235, 958866.6753, 1515835.2069, 19265390.3976, 606725.3087, 1801778.3322, 934592.7996, 8617547.7310, -65919093.5252, 1441395.6510], [ 13040296.2262, 2005194.5764, 1131907.2743, 231618.9579, 6929075.4620, 2413923.3304, 3220089.1130, 664173.2866, 1317013.8687, 43924717.9500, 11796321.7380, 2315328.7151, 10514726.4429, 4010221.4303, 2056767.1888, 2193220.7099, 11714248.2474, 820580.2399, 3048964.0446, -100242523.5904] ] / (2048*2048*2048): logPAM1 := NewLogPAM1: # Human mitochondrial DNA count matrix (based on very short PAM evolution) # taken from 86 full mtDNA genomes (also used for Eve's tree) HumanMtDNA := [ [438851,0,0,0,74,0,0,997,0,0,0,0,0,0,0,0,56.5,0,0,0], [0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [74,0,0,0,444246,0,0,16.5,0,0,0,0,0,0,0,0,1199,0,0,0], [0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0], [997,0,0,0,16.5,0,0,186126,0,0,0,0,0,0,0,0,4,0,0,0], [0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0], [56.5,0,0,0,1199,0,0,4,0,0,0,0,0,0,0,0,350736,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1]]: # RNA viruses. Count matrix taken from 50 RNA viruses ViralRNA := [ [72271,0,0,0,10471,0,0,14868.5,0,0,0,0,0,0,0,0,11546.5,0,0,0], [0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [10471,0,0,0,45021,0,0,6789,0,0,0,0,0,0,0,0,13742,0,0,0], [0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0], [14868.5,0,0,0,6789,0,0,57924,0,0,0,0,0,0,0,0,7237.5,0,0,0], [0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0], [11546.5,0,0,0,13742,0,0,7237.5,0,0,0,0,0,0,0,0,73792,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1]]: BacterialtRNA:=[ [4641,0,0,0,139.5,0,0,1247.5,0,0,0,0,0,0,0,0,187.5,0,0,0], [0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [139.5,0,0,0,6175,0,0,157.5,0,0,0,0,0,0,0,0,911.5,0,0,0], [0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0], [1247.5,0,0,0,157.5,0,0,8287,0,0,0,0,0,0,0,0,151.5,0,0,0], [0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0], [187.5,0,0,0,911.5,0,0,151.5,0,0,0,0,0,0,0,0,5700,0,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0], [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1]]: latex := noeval(ReadLibrary(LaTeXCTools, latex)): LaTeX := noeval(ReadLibrary(LaTeXCTools, LaTeX)): LaTeXC := noeval(ReadLibrary(LaTeXCTools, LaTeXC)): MAlign := noeval(ReadLibrary(MSA, MAlign)): MAlignment := noeval(ReadLibrary(MSA, MAlignment)): PartialOrder := noeval(ReadLibrary(PartialOrder)): PartialOrderMSA := noeval(ReadLibrary(PartialOrder, PartialOrderMSA)): PartialOrderMSA_MAlign := noeval(ReadLibrary(PartialOrder, PartialOrderMSA_MAlign)): SeqThread := noeval(ReadLibrary(PartialOrder, SeqThread)): DynProgBoth_PartOrd_G := noeval(ReadLibrary(DynProgBoth_PartOrd)): DynProgBoth_PartOrd_D := noeval(ReadLibrary(DynProgBoth_PartOrd_D)): # Codon Transition Matrices # Adrian Schneider, 2004 # edited April 2005 and August 2006 CreateCodonMatrices := noeval(ReadLibrary(CodonMatrix,CreateCodonMatrices)): CreateSynMatrices := noeval(ReadLibrary(CodonMatrix,CreateSynMatrices)): CodonPamToPam := noeval(ReadLibrary(CodonMatrix,CodonPamToPam)): PamToCodonPam := noeval(ReadLibrary(CodonMatrix,PamToCodonPam)): CodonAlign := noeval(ReadLibrary(CodonAlign,CodonAlign)): CodonDynProgStrings := noeval(ReadLibrary(CodonAlign,CodonDynProgStrings)): PrintCodonAlignment := noeval(ReadLibrary(CodonAlign,PrintCodonAlignment)): CodonMutate := noeval(ReadLibrary(CodonMutate,CodonMutate)): ScoreAlignment := noeval(ReadLibrary(CodonScore,ScoreAlignment)): EstimateSynPAM := noeval(ReadLibrary(CodonScore,EstimateSynPAM)): EstimateCodonPAM := noeval(ReadLibrary(CodonScore,EstimateCodonPAM)): EstimateNG86 := noeval(ReadLibrary(NeiGojobori,EstimateNG86)): EstimatePB93 := noeval(ReadLibrary(PamiloBianchi,EstimatePB93)): # Boostrapping trees, added by AS BootstrapTree := noeval(ReadLibrary(BootstrapTree,BootstrapTree)): ShowBootstrap := noeval(ReadLibrary(BootstrapTree,ShowBootstrap)): # Gene Ontologies, added by AS, Sept 2005 GOdownload := noeval(ReadLibrary(Ontology,GOdownload)): GOdefinition := noeval(ReadLibrary(Ontology,GOdefinition)): GOname := noeval(ReadLibrary(Ontology,GOname)): GOsubclass := noeval(ReadLibrary(Ontology,GOsubclass)): GOsubclassR := noeval(ReadLibrary(Ontology,GOsubclassR)): GOsuperclassR := noeval(ReadLibrary(Ontology,GOsuperclassR)): GOsuperclass := noeval(ReadLibrary(Ontology,GOsuperclass)): GOnumber := noeval(ReadLibrary(Ontology,GOnumber)): # Rotate Trees, added by CD, Oct 2005 RotateTree := noeval(ReadLibrary(RotateTree,RotateTree)): AllRootedTrees := noeval(ReadLibrary(RotateTree,AllRootedTrees)): AllTernaryRoots := noeval(ReadLibrary(RotateTree,AllTernaryRoots)): # SearchAllString, added by AR, Nov 2005 SearchAllString := noeval(ReadLibrary(SearchAllString,SearchAllString)): HammingSearchAllString := noeval(ReadLibrary(SearchAllString,HammingSearchAllString)): # DNA <-> Protein tools, added by AR, Nov 2005 CodonCount := noeval(ReadLibrary(Translate,CodonCount)): CodonUsage := noeval(ReadLibrary(Translate,CodonUsage)): Translate := noeval(ReadLibrary(Translate,Translate)): BackTranslate := noeval(ReadLibrary(Translate,BackTranslate)): ReplaceString := noeval(ReadLibrary(Translate,ReplaceString)): Transcribe := noeval(ReadLibrary(Translate,Transcribe)): BackTranscribe := noeval(ReadLibrary(Translate,BackTranscribe)): # Codon Bias Tools. Added by AR (Dec 2005 - April 2007) RSCU := noeval(ReadLibrary(CodonIndices,RSCU)): ComputeCAI := noeval(ReadLibrary(CodonIndices,ComputeCAI)): ComputeCAIVector := noeval(ReadLibrary(CodonIndices,ComputeCAIVector)): SetupRA := noeval(ReadLibrary(CodonIndices,SetupRA)): ComputeCarboneRA := noeval(ReadLibrary(CodonIndices,ComputeCarboneRA)): RelativeAdaptiveness := noeval(ReadLibrary(CodonIndices,RelativeAdaptiveness)): FindHighlyExpressedGenes := noeval(ReadLibrary(CodonIndices,FindHighlyExpressedGenes)): ComputeFop := noeval(ReadLibrary(CodonIndices,ComputeFop)): ComputeNEC := noeval(ReadLibrary(CodonIndices,ComputeNEC)): NucleotideContent := noeval(ReadLibrary(CodonIndices,NucleotideContent)): ComputeGC3syn := noeval(ReadLibrary(CodonIndices,ComputeGC3syn)): # Ancestor package, addded by AS, Dec 22, 2005 ProbSeq := noeval(ReadLibrary(Ancestor,ProbSeq)): ProbAncestor := noeval(ReadLibrary(Ancestor,ProbAncestor)): PASfromMSA := noeval(ReadLibrary(Ancestor,PASfromMSA)): PASfromTree := noeval(ReadLibrary(Ancestor,PASfromTree)): PSDynProg := noeval(ReadLibrary(Ancestor,PSDynProg)): # Added by AR (Jan 2006) WriteData := noeval(ReadLibrary(ReadData,WriteData)): # Global variable functions by AS, Feb 2006 Globals := noeval(ReadLibrary(Globals,Globals)): UnassignGlobals := noeval(ReadLibrary(Globals,UnassignGlobals)): # Webtools, added by AS, June 6, 2006 ReadURL := noeval(ReadLibrary(WebTools,ReadURL)): DownloadURL := noeval(ReadLibrary(WebTools,DownloadURL)): # MST, added by CD, Dec 2006 MST := noeval(ReadLibrary(Graph,MST)): # Center the "root" of unrooted trees. AR, April 2007 CenterTreeRoot := noeval(ReadLibrary(CenterTreeRoot,CenterTreeRoot)): TreeSize := noeval(ReadLibrary(CenterTreeRoot,TreeSize)): ReadLibrary('Wrappers/wrapperinit'): # Romberg, added by CD, Dec 2007 Romberg := noeval(ReadLibrary(Integrate)): # UnionFind, added by AA, March 2008 UnionFind := noeval(ReadLibrary(UnionFind)): # ConcatStrings, added by CD, May 2008 ConcatStrings := noeval(ReadLibrary(ConcatStrings)): trim := noeval(ReadLibrary(StringManipulation, trim)): # RobinsonFoulds, added by AA, Jul 2008 RobinsonFoulds := noeval(ReadLibrary(RobinsonFoulds)): IntraDistance := noeval(ReadLibrary(IntraDistance)): BipartiteSquared := noeval(ReadLibrary(BipartiteSquared)): EvolutionaryOptimization := noeval(ReadLibrary(EvolutionaryOptimization)): EvoMinimize := noeval(ReadLibrary(EvoMinimize)): ProbabilisticFA := noeval(ReadLibrary(ProbabilisticFA)): CompressedPFA := noeval(ReadLibrary(ProbabilisticFA,CompressedPFA)): SparsePFA := noeval(ReadLibrary(ProbabilisticFA,SparsePFA)): # RedoCompletion, added by CD, Aug 2008 RedoCompletion := noeval(ReadLibrary(RedoCompletion)): # TaxonID - 5letter mapping SpeciesCode := noeval(ReadLibrary(TaxTools, SpeciesCode)): TaxonId := noeval(ReadLibrary(TaxTools, TaxonId)): UpdateSpeciesCode := noeval(ReadLibrary(TaxTools, UpdateSpeciesCode)): Tax2Five := noeval(ReadLibrary(TaxTools,Tax2Five)): # backward compatibility Five2Tax := noeval(ReadLibrary(TaxTools,Five2Tax)): # backward compatibility # PruneTree, added by AA, Jan 06, 2009 PruneTree := noeval(ReadLibrary(Tree, PruneTree)): # ReconcileTree, added by AA, Jan 06, 2009 ReconcileTree := noeval(ReadLibrary(Reconcile,ReconcileTree)): MLBranches := noeval(ReadLibrary(MLBranches)): # Rank, added by AA, Feb 18. 2009 Rank := noeval(ReadLibrary(Rank, Rank)): # cor, added by AA, Feb 18 2009 cor := noeval(ReadLibrary(Stat,cor)): # MySql wrapper, added by AA, May 13, 2009 MySql := noeval(ReadLibrary(MySQL, MySql)): MySqlResult := noeval(ReadLibrary(MySQL, MySqlResult)): # BirthDeathTree, added by DD, May 26 2010 BirthDeathTree := noeval(ReadLibrary(BirthDeathTree, BirthDeathTree)): ScaleTree := noeval(ReadLibrary(BirthDeathTree, ScaleTree)): ScaleTreeLength := noeval(ReadLibrary(BirthDeathTree, ScaleTreeLength)): AddDeviation := noeval(ReadLibrary(BirthDeathTree, AddDeviation)): LoadMatrixFile := noeval(ReadLibrary(LoadMatrixFile, LoadMatrixFile)): CreateCodonModelMatrices := noeval(ReadLibrary(YangModels, CreateCodonModelMatrices)): CreateParametricQMatrix := noeval(ReadLibrary(YangModels, CreateParametricQMatrix)): GammaRates := noeval(ReadLibrary(GammaRates)): CreateNucleotideMatrices := noeval(ReadLibrary(NucleotideMatrix, CreateNucleotideMatrices)): NucToNInt := noeval(ReadLibrary(NucleotideMatrix, NucToNInt)): NIntToNuc := noeval(ReadLibrary(NucleotideMatrix, NIntToNuc)): NucleotideMutate := noeval(ReadLibrary(NucleotideMatrix, NucleotideMutate)): WriteSeqXML := noeval(ReadLibrary(DBConverters, WriteSeqXML)): RenderTemplate := noeval(ReadLibrary(RenderTemplate, RenderTemplate)): Graph_XGMML := noeval(ReadLibrary(Graph,Graph_XGMML)): Tag := noeval(ReadLibrary(Tag,Tag)): TagNV := noeval(ReadLibrary(Tag,TagNV)): TagTable := noeval(ReadLibrary(Tag,TagTable)): # KHTest by Wang Bo, Dec 2011 KHTest := noeval(ReadLibrary(KHTest, KHTest)): ReadFastaIntoMAlignment := noeval(ReadLibrary(KHTest, ReadFastaIntoMAlignment)): MLTopoTest := noeval(ReadLibrary(KHTest, MLTopoTest)): # Ancestral Recombination Graph ARG := noeval(ReadLibrary(AncestralRecombinationGraph)): RecombinationNode := noeval(ReadLibrary(AncestralRecombinationGraph, RecombinationNode)): CoalescentNode := noeval(ReadLibrary(AncestralRecombinationGraph, CoalescentNode)): LeafNode := noeval(ReadLibrary(AncestralRecombinationGraph, LeafNode)): GraphViz_ARG := noeval(ReadLibrary(AncestralRecombinationGraph, GraphViz_ARG)): # Scientific Databases SDB_Usage := noeval(ReadLibrary(SDB,SDB_Usage)): SDB_Store := noeval(ReadLibrary(SDB,SDB_Store)): SDB_StoreAttribute := noeval(ReadLibrary(SDB,SDB_StoreAttribute)): SDB_Retrieve := noeval(ReadLibrary(SDB,SDB_Retrieve)): SDB_RetrieveFile := noeval(ReadLibrary(SDB,SDB_RetrieveFile)): SDB_EraseFile := noeval(ReadLibrary(SDB,SDB_EraseFile)): SDB_Output := noeval(ReadLibrary(SDB,SDB_Output)): SDB_Flush := noeval(ReadLibrary(SDB,SDB_Flush)): MatchRegex := proc( pattern:string, txt:string) option builtin; 248 end: ZmqRequest := proc( endpoint:string, msg:string) option builtin; 249 end: TaxonomyEntry := noeval(ReadLibrary('Taxonomy',TaxonomyEntry)): TaxonomyDownload := noeval(ReadLibrary('Taxonomy',TaxonomyDownload)): json := noeval(ReadLibrary('json',json)): DetectRepeats := noeval(ReadLibrary(DetectRepeats,DetectRepeats)): DetectRepeatsInSeqs := noeval(ReadLibrary(DetectRepeats,DetectRepeatsInSeqs)): WriteTreks := noeval(ReadLibrary(DetectRepeats,WriteTreks)):